Starting phenix.real_space_refine on Sun Jul 5 17:25:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hw1_35080/07_2026/8hw1_35080.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hw1_35080/07_2026/8hw1_35080.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hw1_35080/07_2026/8hw1_35080.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hw1_35080/07_2026/8hw1_35080.map" model { file = "/net/cci-nas-00/data/ceres_data/8hw1_35080/07_2026/8hw1_35080.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hw1_35080/07_2026/8hw1_35080.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8hw1_35080/07_2026/8hw1_35080.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hw1_35080/07_2026/8hw1_35080.cif" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 121 5.21 5 S 55 5.16 5 C 20592 2.51 5 N 4015 2.21 5 O 4488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 275 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29271 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1886 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 16, 'TRANS': 224} Chain: "A" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 775 Unusual residues: {'32N': 1, 'CLA': 11, 'XAT': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K Time building chain proxies: 4.15, per 1000 atoms: 0.14 Number of scatterers: 29271 At special positions: 0 Unit cell: (196.62, 197.75, 67.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 55 16.00 Mg 121 11.99 O 4488 8.00 N 4015 7.00 C 20592 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=44, symmetry=0 Number of additional bonds: simple=44, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.25 Conformation dependent library (CDL) restraints added in 1.0 seconds 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4752 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 0 sheets defined 56.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 111 through 143 removed outlier: 3.862A pdb=" N SER A 115 " --> pdb=" O ASN A 111 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU A 117 " --> pdb=" O ASP A 113 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 130 " --> pdb=" O TYR A 126 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 133 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 136 " --> pdb=" O MET A 132 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL A 141 " --> pdb=" O GLY A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 156 removed outlier: 3.566A pdb=" N LEU A 156 " --> pdb=" O PRO A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 186 removed outlier: 3.574A pdb=" N LYS A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 240 removed outlier: 3.675A pdb=" N VAL A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG A 221 " --> pdb=" O GLN A 217 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU A 228 " --> pdb=" O ARG A 224 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 254 removed outlier: 3.659A pdb=" N ASP A 250 " --> pdb=" O GLU A 246 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER A 254 " --> pdb=" O ASP A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 removed outlier: 3.625A pdb=" N THR A 262 " --> pdb=" O ASN A 259 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR A 263 " --> pdb=" O ILE A 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 259 through 263' Processing helix chain 'A' and resid 265 through 279 removed outlier: 3.567A pdb=" N VAL A 271 " --> pdb=" O GLY A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 290 removed outlier: 3.779A pdb=" N ILE A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 143 removed outlier: 3.861A pdb=" N SER B 115 " --> pdb=" O ASN B 111 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU B 117 " --> pdb=" O ASP B 113 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B 130 " --> pdb=" O TYR B 126 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU B 133 " --> pdb=" O ARG B 129 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL B 136 " --> pdb=" O MET B 132 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL B 141 " --> pdb=" O GLY B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 156 removed outlier: 3.566A pdb=" N LEU B 156 " --> pdb=" O PRO B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 186 removed outlier: 3.574A pdb=" N LYS B 180 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 240 removed outlier: 3.675A pdb=" N VAL B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG B 221 " --> pdb=" O GLN B 217 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU B 228 " --> pdb=" O ARG B 224 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TRP B 238 " --> pdb=" O SER B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 254 removed outlier: 3.659A pdb=" N ASP B 250 " --> pdb=" O GLU B 246 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER B 254 " --> pdb=" O ASP B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 263 removed outlier: 3.624A pdb=" N THR B 262 " --> pdb=" O ASN B 259 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR B 263 " --> pdb=" O ILE B 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 259 through 263' Processing helix chain 'B' and resid 265 through 279 removed outlier: 3.567A pdb=" N VAL B 271 " --> pdb=" O GLY B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 290 removed outlier: 3.779A pdb=" N ILE B 283 " --> pdb=" O ALA B 279 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 143 removed outlier: 3.862A pdb=" N SER C 115 " --> pdb=" O ASN C 111 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU C 117 " --> pdb=" O ASP C 113 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU C 130 " --> pdb=" O TYR C 126 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU C 133 " --> pdb=" O ARG C 129 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL C 136 " --> pdb=" O MET C 132 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL C 141 " --> pdb=" O GLY C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 156 removed outlier: 3.567A pdb=" N LEU C 156 " --> pdb=" O PRO C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 186 removed outlier: 3.574A pdb=" N LYS C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG C 186 " --> pdb=" O LEU C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 240 removed outlier: 3.675A pdb=" N VAL C 220 " --> pdb=" O ARG C 216 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG C 221 " --> pdb=" O GLN C 217 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU C 228 " --> pdb=" O ARG C 224 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP C 238 " --> pdb=" O SER C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 254 removed outlier: 3.659A pdb=" N ASP C 250 " --> pdb=" O GLU C 246 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER C 254 " --> pdb=" O ASP C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 263 removed outlier: 3.625A pdb=" N THR C 262 " --> pdb=" O ASN C 259 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR C 263 " --> pdb=" O ILE C 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 259 through 263' Processing helix chain 'C' and resid 265 through 279 removed outlier: 3.567A pdb=" N VAL C 271 " --> pdb=" O GLY C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 290 removed outlier: 3.779A pdb=" N ILE C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 143 removed outlier: 3.862A pdb=" N SER D 115 " --> pdb=" O ASN D 111 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU D 117 " --> pdb=" O ASP D 113 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU D 130 " --> pdb=" O TYR D 126 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU D 133 " --> pdb=" O ARG D 129 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL D 136 " --> pdb=" O MET D 132 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL D 141 " --> pdb=" O GLY D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 156 removed outlier: 3.566A pdb=" N LEU D 156 " --> pdb=" O PRO D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 186 removed outlier: 3.574A pdb=" N LYS D 180 " --> pdb=" O LEU D 176 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 240 removed outlier: 3.675A pdb=" N VAL D 220 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG D 221 " --> pdb=" O GLN D 217 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU D 228 " --> pdb=" O ARG D 224 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP D 238 " --> pdb=" O SER D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 254 removed outlier: 3.659A pdb=" N ASP D 250 " --> pdb=" O GLU D 246 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER D 254 " --> pdb=" O ASP D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 263 removed outlier: 3.625A pdb=" N THR D 262 " --> pdb=" O ASN D 259 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR D 263 " --> pdb=" O ILE D 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 259 through 263' Processing helix chain 'D' and resid 265 through 279 removed outlier: 3.567A pdb=" N VAL D 271 " --> pdb=" O GLY D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 290 removed outlier: 3.778A pdb=" N ILE D 283 " --> pdb=" O ALA D 279 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 143 removed outlier: 3.861A pdb=" N SER E 115 " --> pdb=" O ASN E 111 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU E 117 " --> pdb=" O ASP E 113 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU E 130 " --> pdb=" O TYR E 126 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU E 133 " --> pdb=" O ARG E 129 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL E 136 " --> pdb=" O MET E 132 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL E 141 " --> pdb=" O GLY E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 156 removed outlier: 3.566A pdb=" N LEU E 156 " --> pdb=" O PRO E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 186 removed outlier: 3.574A pdb=" N LYS E 180 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG E 186 " --> pdb=" O LEU E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 240 removed outlier: 3.675A pdb=" N VAL E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG E 221 " --> pdb=" O GLN E 217 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU E 228 " --> pdb=" O ARG E 224 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP E 238 " --> pdb=" O SER E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 254 removed outlier: 3.659A pdb=" N ASP E 250 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER E 254 " --> pdb=" O ASP E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 263 removed outlier: 3.624A pdb=" N THR E 262 " --> pdb=" O ASN E 259 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR E 263 " --> pdb=" O ILE E 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 259 through 263' Processing helix chain 'E' and resid 265 through 279 removed outlier: 3.567A pdb=" N VAL E 271 " --> pdb=" O GLY E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 290 removed outlier: 3.779A pdb=" N ILE E 283 " --> pdb=" O ALA E 279 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS E 290 " --> pdb=" O LEU E 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 143 removed outlier: 3.861A pdb=" N SER F 115 " --> pdb=" O ASN F 111 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU F 117 " --> pdb=" O ASP F 113 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU F 130 " --> pdb=" O TYR F 126 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU F 133 " --> pdb=" O ARG F 129 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL F 136 " --> pdb=" O MET F 132 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL F 141 " --> pdb=" O GLY F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 156 removed outlier: 3.566A pdb=" N LEU F 156 " --> pdb=" O PRO F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 186 removed outlier: 3.574A pdb=" N LYS F 180 " --> pdb=" O LEU F 176 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG F 186 " --> pdb=" O LEU F 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 240 removed outlier: 3.675A pdb=" N VAL F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG F 221 " --> pdb=" O GLN F 217 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU F 228 " --> pdb=" O ARG F 224 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP F 238 " --> pdb=" O SER F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 254 removed outlier: 3.659A pdb=" N ASP F 250 " --> pdb=" O GLU F 246 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER F 254 " --> pdb=" O ASP F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 263 removed outlier: 3.625A pdb=" N THR F 262 " --> pdb=" O ASN F 259 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR F 263 " --> pdb=" O ILE F 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 259 through 263' Processing helix chain 'F' and resid 265 through 279 removed outlier: 3.567A pdb=" N VAL F 271 " --> pdb=" O GLY F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 290 removed outlier: 3.779A pdb=" N ILE F 283 " --> pdb=" O ALA F 279 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS F 290 " --> pdb=" O LEU F 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 143 removed outlier: 3.862A pdb=" N SER G 115 " --> pdb=" O ASN G 111 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU G 117 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU G 130 " --> pdb=" O TYR G 126 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU G 133 " --> pdb=" O ARG G 129 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL G 136 " --> pdb=" O MET G 132 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL G 141 " --> pdb=" O GLY G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 156 removed outlier: 3.567A pdb=" N LEU G 156 " --> pdb=" O PRO G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 186 removed outlier: 3.574A pdb=" N LYS G 180 " --> pdb=" O LEU G 176 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG G 186 " --> pdb=" O LEU G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 240 removed outlier: 3.675A pdb=" N VAL G 220 " --> pdb=" O ARG G 216 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG G 221 " --> pdb=" O GLN G 217 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU G 228 " --> pdb=" O ARG G 224 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP G 238 " --> pdb=" O SER G 234 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 254 removed outlier: 3.659A pdb=" N ASP G 250 " --> pdb=" O GLU G 246 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER G 254 " --> pdb=" O ASP G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 259 through 263 removed outlier: 3.625A pdb=" N THR G 262 " --> pdb=" O ASN G 259 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR G 263 " --> pdb=" O ILE G 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 259 through 263' Processing helix chain 'G' and resid 265 through 279 removed outlier: 3.567A pdb=" N VAL G 271 " --> pdb=" O GLY G 267 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 290 removed outlier: 3.779A pdb=" N ILE G 283 " --> pdb=" O ALA G 279 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS G 290 " --> pdb=" O LEU G 286 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 143 removed outlier: 3.862A pdb=" N SER H 115 " --> pdb=" O ASN H 111 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU H 117 " --> pdb=" O ASP H 113 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU H 130 " --> pdb=" O TYR H 126 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU H 133 " --> pdb=" O ARG H 129 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL H 136 " --> pdb=" O MET H 132 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL H 141 " --> pdb=" O GLY H 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 152 through 156 removed outlier: 3.567A pdb=" N LEU H 156 " --> pdb=" O PRO H 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 186 removed outlier: 3.574A pdb=" N LYS H 180 " --> pdb=" O LEU H 176 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG H 186 " --> pdb=" O LEU H 182 " (cutoff:3.500A) Processing helix chain 'H' and resid 214 through 240 removed outlier: 3.675A pdb=" N VAL H 220 " --> pdb=" O ARG H 216 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG H 221 " --> pdb=" O GLN H 217 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU H 228 " --> pdb=" O ARG H 224 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP H 238 " --> pdb=" O SER H 234 " (cutoff:3.500A) Processing helix chain 'H' and resid 243 through 254 removed outlier: 3.659A pdb=" N ASP H 250 " --> pdb=" O GLU H 246 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER H 254 " --> pdb=" O ASP H 250 " (cutoff:3.500A) Processing helix chain 'H' and resid 259 through 263 removed outlier: 3.625A pdb=" N THR H 262 " --> pdb=" O ASN H 259 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR H 263 " --> pdb=" O ILE H 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 259 through 263' Processing helix chain 'H' and resid 265 through 279 removed outlier: 3.567A pdb=" N VAL H 271 " --> pdb=" O GLY H 267 " (cutoff:3.500A) Processing helix chain 'H' and resid 279 through 290 removed outlier: 3.779A pdb=" N ILE H 283 " --> pdb=" O ALA H 279 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS H 290 " --> pdb=" O LEU H 286 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 143 removed outlier: 3.861A pdb=" N SER I 115 " --> pdb=" O ASN I 111 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU I 117 " --> pdb=" O ASP I 113 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU I 130 " --> pdb=" O TYR I 126 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU I 133 " --> pdb=" O ARG I 129 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL I 136 " --> pdb=" O MET I 132 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL I 141 " --> pdb=" O GLY I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 156 removed outlier: 3.566A pdb=" N LEU I 156 " --> pdb=" O PRO I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 186 removed outlier: 3.575A pdb=" N LYS I 180 " --> pdb=" O LEU I 176 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG I 186 " --> pdb=" O LEU I 182 " (cutoff:3.500A) Processing helix chain 'I' and resid 214 through 240 removed outlier: 3.675A pdb=" N VAL I 220 " --> pdb=" O ARG I 216 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG I 221 " --> pdb=" O GLN I 217 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU I 228 " --> pdb=" O ARG I 224 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP I 238 " --> pdb=" O SER I 234 " (cutoff:3.500A) Processing helix chain 'I' and resid 243 through 254 removed outlier: 3.659A pdb=" N ASP I 250 " --> pdb=" O GLU I 246 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER I 254 " --> pdb=" O ASP I 250 " (cutoff:3.500A) Processing helix chain 'I' and resid 259 through 263 removed outlier: 3.625A pdb=" N THR I 262 " --> pdb=" O ASN I 259 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR I 263 " --> pdb=" O ILE I 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 259 through 263' Processing helix chain 'I' and resid 265 through 279 removed outlier: 3.567A pdb=" N VAL I 271 " --> pdb=" O GLY I 267 " (cutoff:3.500A) Processing helix chain 'I' and resid 279 through 290 removed outlier: 3.779A pdb=" N ILE I 283 " --> pdb=" O ALA I 279 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS I 290 " --> pdb=" O LEU I 286 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 143 removed outlier: 3.861A pdb=" N SER J 115 " --> pdb=" O ASN J 111 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU J 117 " --> pdb=" O ASP J 113 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU J 130 " --> pdb=" O TYR J 126 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU J 133 " --> pdb=" O ARG J 129 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL J 136 " --> pdb=" O MET J 132 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL J 141 " --> pdb=" O GLY J 137 " (cutoff:3.500A) Processing helix chain 'J' and resid 152 through 156 removed outlier: 3.567A pdb=" N LEU J 156 " --> pdb=" O PRO J 153 " (cutoff:3.500A) Processing helix chain 'J' and resid 160 through 186 removed outlier: 3.574A pdb=" N LYS J 180 " --> pdb=" O LEU J 176 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG J 186 " --> pdb=" O LEU J 182 " (cutoff:3.500A) Processing helix chain 'J' and resid 214 through 240 removed outlier: 3.675A pdb=" N VAL J 220 " --> pdb=" O ARG J 216 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG J 221 " --> pdb=" O GLN J 217 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU J 228 " --> pdb=" O ARG J 224 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP J 238 " --> pdb=" O SER J 234 " (cutoff:3.500A) Processing helix chain 'J' and resid 243 through 254 removed outlier: 3.659A pdb=" N ASP J 250 " --> pdb=" O GLU J 246 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER J 254 " --> pdb=" O ASP J 250 " (cutoff:3.500A) Processing helix chain 'J' and resid 259 through 263 removed outlier: 3.625A pdb=" N THR J 262 " --> pdb=" O ASN J 259 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR J 263 " --> pdb=" O ILE J 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 259 through 263' Processing helix chain 'J' and resid 265 through 279 removed outlier: 3.568A pdb=" N VAL J 271 " --> pdb=" O GLY J 267 " (cutoff:3.500A) Processing helix chain 'J' and resid 279 through 290 removed outlier: 3.779A pdb=" N ILE J 283 " --> pdb=" O ALA J 279 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS J 290 " --> pdb=" O LEU J 286 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 143 removed outlier: 3.862A pdb=" N SER K 115 " --> pdb=" O ASN K 111 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU K 117 " --> pdb=" O ASP K 113 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU K 130 " --> pdb=" O TYR K 126 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU K 133 " --> pdb=" O ARG K 129 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL K 136 " --> pdb=" O MET K 132 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL K 141 " --> pdb=" O GLY K 137 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 156 removed outlier: 3.567A pdb=" N LEU K 156 " --> pdb=" O PRO K 153 " (cutoff:3.500A) Processing helix chain 'K' and resid 160 through 186 removed outlier: 3.574A pdb=" N LYS K 180 " --> pdb=" O LEU K 176 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG K 186 " --> pdb=" O LEU K 182 " (cutoff:3.500A) Processing helix chain 'K' and resid 214 through 240 removed outlier: 3.675A pdb=" N VAL K 220 " --> pdb=" O ARG K 216 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG K 221 " --> pdb=" O GLN K 217 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU K 228 " --> pdb=" O ARG K 224 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP K 238 " --> pdb=" O SER K 234 " (cutoff:3.500A) Processing helix chain 'K' and resid 243 through 254 removed outlier: 3.660A pdb=" N ASP K 250 " --> pdb=" O GLU K 246 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER K 254 " --> pdb=" O ASP K 250 " (cutoff:3.500A) Processing helix chain 'K' and resid 259 through 263 removed outlier: 3.624A pdb=" N THR K 262 " --> pdb=" O ASN K 259 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR K 263 " --> pdb=" O ILE K 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 259 through 263' Processing helix chain 'K' and resid 265 through 279 removed outlier: 3.567A pdb=" N VAL K 271 " --> pdb=" O GLY K 267 " (cutoff:3.500A) Processing helix chain 'K' and resid 279 through 290 removed outlier: 3.779A pdb=" N ILE K 283 " --> pdb=" O ALA K 279 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS K 290 " --> pdb=" O LEU K 286 " (cutoff:3.500A) 946 hydrogen bonds defined for protein. 2805 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.32 Time building geometry restraints manager: 4.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.35: 8287 1.35 - 1.51: 13747 1.51 - 1.67: 8304 1.67 - 1.83: 99 1.83 - 1.99: 484 Bond restraints: 30921 Sorted by residual: bond pdb=" CAD CLA H 610 " pdb=" CBD CLA H 610 " ideal model delta sigma weight residual 1.563 1.414 0.149 2.00e-02 2.50e+03 5.56e+01 bond pdb=" CAD CLA I 610 " pdb=" CBD CLA I 610 " ideal model delta sigma weight residual 1.563 1.414 0.149 2.00e-02 2.50e+03 5.55e+01 bond pdb=" CAD CLA E 610 " pdb=" CBD CLA E 610 " ideal model delta sigma weight residual 1.563 1.414 0.149 2.00e-02 2.50e+03 5.55e+01 bond pdb=" CAD CLA B 610 " pdb=" CBD CLA B 610 " ideal model delta sigma weight residual 1.563 1.414 0.149 2.00e-02 2.50e+03 5.55e+01 bond pdb=" CAD CLA K 610 " pdb=" CBD CLA K 610 " ideal model delta sigma weight residual 1.563 1.414 0.149 2.00e-02 2.50e+03 5.54e+01 ... (remaining 30916 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.11: 41748 4.11 - 8.21: 1933 8.21 - 12.32: 110 12.32 - 16.42: 66 16.42 - 20.53: 88 Bond angle restraints: 43945 Sorted by residual: angle pdb=" NB CLA B 603 " pdb="MG CLA B 603 " pdb=" ND CLA B 603 " ideal model delta sigma weight residual 176.90 156.37 20.53 3.00e+00 1.11e-01 4.68e+01 angle pdb=" NB CLA J 603 " pdb="MG CLA J 603 " pdb=" ND CLA J 603 " ideal model delta sigma weight residual 176.90 156.39 20.51 3.00e+00 1.11e-01 4.67e+01 angle pdb=" NB CLA C 603 " pdb="MG CLA C 603 " pdb=" ND CLA C 603 " ideal model delta sigma weight residual 176.90 156.40 20.50 3.00e+00 1.11e-01 4.67e+01 angle pdb=" NB CLA E 603 " pdb="MG CLA E 603 " pdb=" ND CLA E 603 " ideal model delta sigma weight residual 176.90 156.41 20.49 3.00e+00 1.11e-01 4.67e+01 angle pdb=" NB CLA I 603 " pdb="MG CLA I 603 " pdb=" ND CLA I 603 " ideal model delta sigma weight residual 176.90 156.41 20.49 3.00e+00 1.11e-01 4.67e+01 ... (remaining 43940 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.20: 12145 20.20 - 40.40: 1594 40.40 - 60.60: 748 60.60 - 80.80: 121 80.80 - 101.00: 55 Dihedral angle restraints: 14663 sinusoidal: 7205 harmonic: 7458 Sorted by residual: dihedral pdb=" CA GLY E 145 " pdb=" C GLY E 145 " pdb=" N LYS E 146 " pdb=" CA LYS E 146 " ideal model delta harmonic sigma weight residual -180.00 -158.83 -21.17 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA GLY J 145 " pdb=" C GLY J 145 " pdb=" N LYS J 146 " pdb=" CA LYS J 146 " ideal model delta harmonic sigma weight residual 180.00 -158.83 -21.17 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA GLY B 145 " pdb=" C GLY B 145 " pdb=" N LYS B 146 " pdb=" CA LYS B 146 " ideal model delta harmonic sigma weight residual -180.00 -158.84 -21.16 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 14660 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 3051 0.087 - 0.175: 427 0.175 - 0.262: 137 0.262 - 0.349: 80 0.349 - 0.437: 23 Chirality restraints: 3718 Sorted by residual: chirality pdb=" C29 32N B 613 " pdb=" C28 32N B 613 " pdb=" C30 32N B 613 " pdb=" C34 32N B 613 " both_signs ideal model delta sigma weight residual False -2.44 -2.00 -0.44 2.00e-01 2.50e+01 4.76e+00 chirality pdb=" C29 32N I 613 " pdb=" C28 32N I 613 " pdb=" C30 32N I 613 " pdb=" C34 32N I 613 " both_signs ideal model delta sigma weight residual False -2.44 -2.00 -0.44 2.00e-01 2.50e+01 4.75e+00 chirality pdb=" C29 32N D 613 " pdb=" C28 32N D 613 " pdb=" C30 32N D 613 " pdb=" C34 32N D 613 " both_signs ideal model delta sigma weight residual False -2.44 -2.00 -0.44 2.00e-01 2.50e+01 4.73e+00 ... (remaining 3715 not shown) Planarity restraints: 5852 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1A CLA H 606 " -0.027 2.00e-02 2.50e+03 2.08e-01 6.47e+02 pdb=" C2A CLA H 606 " -0.301 2.00e-02 2.50e+03 pdb=" C4A CLA H 606 " 0.284 2.00e-02 2.50e+03 pdb=" CHA CLA H 606 " 0.213 2.00e-02 2.50e+03 pdb=" NA CLA H 606 " 0.032 2.00e-02 2.50e+03 pdb="MG CLA H 606 " -0.201 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A CLA C 606 " 0.027 2.00e-02 2.50e+03 2.08e-01 6.47e+02 pdb=" C2A CLA C 606 " 0.301 2.00e-02 2.50e+03 pdb=" C4A CLA C 606 " -0.284 2.00e-02 2.50e+03 pdb=" CHA CLA C 606 " -0.213 2.00e-02 2.50e+03 pdb=" NA CLA C 606 " -0.032 2.00e-02 2.50e+03 pdb="MG CLA C 606 " 0.201 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A CLA F 606 " 0.027 2.00e-02 2.50e+03 2.08e-01 6.47e+02 pdb=" C2A CLA F 606 " 0.301 2.00e-02 2.50e+03 pdb=" C4A CLA F 606 " -0.283 2.00e-02 2.50e+03 pdb=" CHA CLA F 606 " -0.213 2.00e-02 2.50e+03 pdb=" NA CLA F 606 " -0.032 2.00e-02 2.50e+03 pdb="MG CLA F 606 " 0.201 2.00e-02 2.50e+03 ... (remaining 5849 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 967 2.69 - 3.24: 24883 3.24 - 3.79: 44951 3.79 - 4.35: 58987 4.35 - 4.90: 101292 Nonbonded interactions: 231080 Sorted by model distance: nonbonded pdb=" O VAL F 271 " pdb=" OG SER F 275 " model vdw 2.137 3.040 nonbonded pdb=" O VAL K 271 " pdb=" OG SER K 275 " model vdw 2.137 3.040 nonbonded pdb=" O VAL B 271 " pdb=" OG SER B 275 " model vdw 2.137 3.040 nonbonded pdb=" O VAL I 271 " pdb=" OG SER I 275 " model vdw 2.137 3.040 nonbonded pdb=" O VAL G 271 " pdb=" OG SER G 275 " model vdw 2.138 3.040 ... (remaining 231075 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 23.280 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.031 0.686 30965 Z= 1.861 Angle : 1.980 20.526 43945 Z= 0.767 Chirality : 0.089 0.437 3718 Planarity : 0.029 0.208 5852 Dihedral : 22.166 100.996 9911 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.30 % Favored : 88.70 % Rotamer: Outliers : 6.74 % Allowed : 7.77 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.15), residues: 2629 helix: -0.39 (0.14), residues: 1309 sheet: None (None), residues: 0 loop : -3.23 (0.14), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG K 116 TYR 0.008 0.001 TYR K 68 PHE 0.022 0.003 PHE I 230 TRP 0.009 0.002 TRP D 69 HIS 0.009 0.003 HIS K 193 Details of bonding type rmsd/Z covalent geometry : bond 0.02444 / 1.22 (30921) covalent geometry : angle 1.98002 / 0.77 (43945) hydrogen bonds : bond 0.17699 / 11.80 ( 946) hydrogen bonds : angle 6.37413 / 4.40 ( 2805) Misc. bond : bond 0.51889 / 32.02 ( 44) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 478 time to evaluate : 0.899 Fit side-chains REVERT: A 57 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6789 (tp30) REVERT: A 115 SER cc_start: 0.8882 (t) cc_final: 0.8646 (m) REVERT: A 132 MET cc_start: 0.8638 (mtm) cc_final: 0.8227 (mtp) REVERT: B 115 SER cc_start: 0.8821 (t) cc_final: 0.8593 (m) REVERT: B 132 MET cc_start: 0.8667 (mtm) cc_final: 0.8258 (mtp) REVERT: B 190 GLU cc_start: 0.8035 (tt0) cc_final: 0.7817 (tt0) REVERT: B 242 LYS cc_start: 0.8743 (mttm) cc_final: 0.8245 (mttt) REVERT: B 290 LYS cc_start: 0.7201 (OUTLIER) cc_final: 0.6846 (ttmt) REVERT: C 200 ASP cc_start: 0.8481 (OUTLIER) cc_final: 0.8138 (t0) REVERT: C 290 LYS cc_start: 0.7269 (OUTLIER) cc_final: 0.6951 (ttpt) REVERT: D 54 MET cc_start: 0.8292 (mtp) cc_final: 0.8024 (mtp) REVERT: D 204 LEU cc_start: 0.8701 (mt) cc_final: 0.8426 (mp) REVERT: E 59 ASP cc_start: 0.8286 (p0) cc_final: 0.8080 (p0) REVERT: E 180 LYS cc_start: 0.8673 (tptt) cc_final: 0.7886 (tptm) REVERT: E 184 ASN cc_start: 0.7965 (m-40) cc_final: 0.7682 (m-40) REVERT: E 200 ASP cc_start: 0.8440 (OUTLIER) cc_final: 0.7989 (t0) REVERT: E 227 MET cc_start: 0.9042 (mtt) cc_final: 0.8769 (mtp) REVERT: F 115 SER cc_start: 0.8836 (t) cc_final: 0.8595 (m) REVERT: F 180 LYS cc_start: 0.8883 (tptt) cc_final: 0.8679 (tptm) REVERT: F 246 GLU cc_start: 0.6896 (mp0) cc_final: 0.6534 (mp0) REVERT: G 132 MET cc_start: 0.8651 (mtm) cc_final: 0.8423 (mtm) REVERT: G 180 LYS cc_start: 0.8675 (tptt) cc_final: 0.7930 (tptm) REVERT: H 132 MET cc_start: 0.8654 (mtm) cc_final: 0.8357 (mtp) REVERT: H 180 LYS cc_start: 0.8796 (tptt) cc_final: 0.8314 (tptm) REVERT: I 102 GLN cc_start: 0.8896 (mt0) cc_final: 0.8444 (mt0) REVERT: I 115 SER cc_start: 0.8850 (t) cc_final: 0.8621 (m) REVERT: I 132 MET cc_start: 0.8622 (mtm) cc_final: 0.8417 (mtp) REVERT: I 180 LYS cc_start: 0.8568 (tptt) cc_final: 0.7772 (tptm) REVERT: I 184 ASN cc_start: 0.7911 (m-40) cc_final: 0.7665 (m110) REVERT: I 190 GLU cc_start: 0.8155 (tt0) cc_final: 0.7845 (tt0) REVERT: I 200 ASP cc_start: 0.8656 (OUTLIER) cc_final: 0.8346 (t0) REVERT: J 132 MET cc_start: 0.8588 (mtm) cc_final: 0.8217 (mtp) REVERT: J 200 ASP cc_start: 0.8560 (OUTLIER) cc_final: 0.8348 (m-30) REVERT: J 242 LYS cc_start: 0.8720 (mttm) cc_final: 0.8147 (mttt) REVERT: K 117 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8280 (mt) REVERT: K 227 MET cc_start: 0.8986 (mtt) cc_final: 0.8727 (mtm) outliers start: 143 outliers final: 43 residues processed: 557 average time/residue: 0.1985 time to fit residues: 175.2424 Evaluate side-chains 448 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 397 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 200 ASP Chi-restraints excluded: chain E residue 257 GLU Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 106 ASP Chi-restraints excluded: chain F residue 257 GLU Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 106 ASP Chi-restraints excluded: chain G residue 257 GLU Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 257 GLU Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 106 ASP Chi-restraints excluded: chain I residue 200 ASP Chi-restraints excluded: chain I residue 257 GLU Chi-restraints excluded: chain I residue 275 SER Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain J residue 106 ASP Chi-restraints excluded: chain J residue 200 ASP Chi-restraints excluded: chain J residue 257 GLU Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain K residue 84 SER Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain K residue 257 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 0.0470 overall best weight: 1.1082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 184 ASN B 184 ASN B 247 ASN C 184 ASN E 236 GLN E 247 ASN F 247 ASN G 236 GLN H 184 ASN I 247 ASN J 247 ASN K 184 ASN K 247 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.132828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.102063 restraints weight = 35733.926| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.70 r_work: 0.2875 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.513 30965 Z= 0.179 Angle : 0.823 9.693 43945 Z= 0.340 Chirality : 0.058 0.413 3718 Planarity : 0.006 0.034 5852 Dihedral : 19.201 101.951 5307 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 1.88 % Allowed : 13.05 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.16), residues: 2629 helix: 0.45 (0.14), residues: 1419 sheet: None (None), residues: 0 loop : -3.19 (0.15), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 89 TYR 0.015 0.002 TYR E 112 PHE 0.013 0.001 PHE J 159 TRP 0.008 0.001 TRP E 100 HIS 0.004 0.001 HIS I 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 (30921) covalent geometry : angle 0.82350 / 0.34 (43945) hydrogen bonds : bond 0.05001 / 3.34 ( 946) hydrogen bonds : angle 4.05242 / 2.85 ( 2805) Misc. bond : bond 0.25308 / 15.91 ( 44) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 435 time to evaluate : 0.888 Fit side-chains REVERT: A 56 GLU cc_start: 0.6934 (mt-10) cc_final: 0.6656 (mt-10) REVERT: A 57 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.6780 (tp30) REVERT: A 106 ASP cc_start: 0.7608 (m-30) cc_final: 0.7272 (t0) REVERT: A 132 MET cc_start: 0.8750 (mtm) cc_final: 0.8326 (mtp) REVERT: A 213 ASP cc_start: 0.9010 (p0) cc_final: 0.8690 (p0) REVERT: B 57 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.6692 (tp30) REVERT: B 115 SER cc_start: 0.8825 (t) cc_final: 0.8554 (m) REVERT: B 132 MET cc_start: 0.8742 (mtm) cc_final: 0.8499 (mtp) REVERT: B 183 GLU cc_start: 0.7953 (tt0) cc_final: 0.7643 (tm-30) REVERT: C 57 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.6730 (tp30) REVERT: C 200 ASP cc_start: 0.8450 (OUTLIER) cc_final: 0.8072 (t0) REVERT: D 54 MET cc_start: 0.8607 (mtp) cc_final: 0.8401 (mtp) REVERT: D 57 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7403 (tp30) REVERT: D 106 ASP cc_start: 0.7637 (m-30) cc_final: 0.7415 (t0) REVERT: D 180 LYS cc_start: 0.8626 (tptt) cc_final: 0.8253 (tptm) REVERT: D 210 LEU cc_start: 0.8811 (mp) cc_final: 0.8410 (mt) REVERT: D 213 ASP cc_start: 0.9023 (p0) cc_final: 0.8812 (p0) REVERT: E 57 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.6944 (tp30) REVERT: E 180 LYS cc_start: 0.8449 (tptt) cc_final: 0.7844 (tptm) REVERT: E 200 ASP cc_start: 0.8551 (OUTLIER) cc_final: 0.8167 (t0) REVERT: E 213 ASP cc_start: 0.9034 (p0) cc_final: 0.8738 (p0) REVERT: F 57 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.6692 (tp30) REVERT: F 106 ASP cc_start: 0.7743 (m-30) cc_final: 0.7478 (t0) REVERT: F 115 SER cc_start: 0.9002 (t) cc_final: 0.8709 (m) REVERT: F 257 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8089 (pm20) REVERT: G 57 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7038 (tp30) REVERT: G 180 LYS cc_start: 0.8468 (tptt) cc_final: 0.7925 (tptm) REVERT: H 180 LYS cc_start: 0.8671 (tptt) cc_final: 0.8265 (tptm) REVERT: I 56 GLU cc_start: 0.7202 (mt-10) cc_final: 0.6987 (mt-10) REVERT: I 57 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.6838 (tp30) REVERT: I 106 ASP cc_start: 0.7703 (m-30) cc_final: 0.7391 (t0) REVERT: I 180 LYS cc_start: 0.8476 (tptt) cc_final: 0.8013 (tptm) REVERT: I 190 GLU cc_start: 0.8352 (tt0) cc_final: 0.7942 (tt0) REVERT: I 200 ASP cc_start: 0.8762 (OUTLIER) cc_final: 0.8365 (t0) REVERT: I 213 ASP cc_start: 0.8866 (p0) cc_final: 0.8612 (p0) REVERT: I 250 ASP cc_start: 0.7841 (m-30) cc_final: 0.7457 (m-30) REVERT: J 57 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.6856 (tp30) REVERT: J 106 ASP cc_start: 0.7888 (m-30) cc_final: 0.7659 (t0) REVERT: J 132 MET cc_start: 0.8810 (mtm) cc_final: 0.8591 (mtp) REVERT: J 242 LYS cc_start: 0.8609 (mttm) cc_final: 0.7834 (mtmt) REVERT: K 142 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7871 (tt0) outliers start: 40 outliers final: 4 residues processed: 460 average time/residue: 0.2057 time to fit residues: 148.3832 Evaluate side-chains 418 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 401 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 200 ASP Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 257 GLU Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 200 ASP Chi-restraints excluded: chain J residue 57 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 190 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 213 optimal weight: 6.9990 chunk 209 optimal weight: 6.9990 chunk 168 optimal weight: 10.0000 chunk 255 optimal weight: 9.9990 chunk 157 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 127 optimal weight: 5.9990 chunk 217 optimal weight: 0.0980 chunk 108 optimal weight: 9.9990 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 184 ASN E 184 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.127849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.097473 restraints weight = 35581.501| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 1.61 r_work: 0.2731 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.534 30965 Z= 0.282 Angle : 0.933 14.248 43945 Z= 0.383 Chirality : 0.063 0.425 3718 Planarity : 0.007 0.051 5852 Dihedral : 18.560 100.644 5228 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 1.51 % Allowed : 15.45 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.16), residues: 2629 helix: 0.51 (0.14), residues: 1430 sheet: None (None), residues: 0 loop : -3.07 (0.16), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 221 TYR 0.015 0.002 TYR G 68 PHE 0.025 0.002 PHE C 230 TRP 0.010 0.002 TRP A 69 HIS 0.012 0.002 HIS I 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00607 / 0.26 (30921) covalent geometry : angle 0.93271 / 0.38 (43945) hydrogen bonds : bond 0.06069 / 4.08 ( 946) hydrogen bonds : angle 3.92854 / 2.76 ( 2805) Misc. bond : bond 0.25842 / 16.28 ( 44) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 427 time to evaluate : 1.107 Fit side-chains REVERT: A 106 ASP cc_start: 0.7580 (m-30) cc_final: 0.7232 (t0) REVERT: A 132 MET cc_start: 0.8777 (mtm) cc_final: 0.8348 (mtp) REVERT: B 115 SER cc_start: 0.8956 (t) cc_final: 0.8650 (m) REVERT: C 200 ASP cc_start: 0.8441 (OUTLIER) cc_final: 0.8003 (t0) REVERT: C 213 ASP cc_start: 0.9110 (p0) cc_final: 0.8906 (p0) REVERT: C 290 LYS cc_start: 0.7356 (mtpp) cc_final: 0.6968 (ttpt) REVERT: D 254 SER cc_start: 0.8390 (p) cc_final: 0.8155 (p) REVERT: E 59 ASP cc_start: 0.8488 (p0) cc_final: 0.8273 (p0) REVERT: E 180 LYS cc_start: 0.8488 (tptt) cc_final: 0.8174 (tptt) REVERT: E 200 ASP cc_start: 0.8435 (OUTLIER) cc_final: 0.8026 (t0) REVERT: E 227 MET cc_start: 0.9273 (mtt) cc_final: 0.9026 (mtp) REVERT: E 290 LYS cc_start: 0.7531 (mtpp) cc_final: 0.7244 (ttmt) REVERT: F 106 ASP cc_start: 0.7853 (m-30) cc_final: 0.7557 (t0) REVERT: F 115 SER cc_start: 0.9198 (t) cc_final: 0.8921 (m) REVERT: G 180 LYS cc_start: 0.8583 (tptt) cc_final: 0.7990 (tptm) REVERT: H 180 LYS cc_start: 0.8731 (tptt) cc_final: 0.8364 (tptm) REVERT: I 102 GLN cc_start: 0.9081 (mt0) cc_final: 0.8856 (mt0) REVERT: I 106 ASP cc_start: 0.7781 (m-30) cc_final: 0.7482 (t0) REVERT: I 180 LYS cc_start: 0.8520 (tptt) cc_final: 0.7980 (tptm) REVERT: I 200 ASP cc_start: 0.8800 (OUTLIER) cc_final: 0.8381 (t0) REVERT: I 213 ASP cc_start: 0.9031 (p0) cc_final: 0.8777 (p0) REVERT: I 250 ASP cc_start: 0.7780 (m-30) cc_final: 0.7420 (m-30) REVERT: J 132 MET cc_start: 0.8812 (mtm) cc_final: 0.8606 (mtm) REVERT: J 183 GLU cc_start: 0.8264 (tm-30) cc_final: 0.8018 (tp30) REVERT: J 254 SER cc_start: 0.8502 (p) cc_final: 0.8252 (p) REVERT: K 111 ASN cc_start: 0.7729 (m-40) cc_final: 0.7525 (m-40) outliers start: 32 outliers final: 18 residues processed: 446 average time/residue: 0.1781 time to fit residues: 128.2866 Evaluate side-chains 426 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 405 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 200 ASP Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 257 GLU Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain I residue 200 ASP Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 187 GLU Chi-restraints excluded: chain K residue 64 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 135 optimal weight: 6.9990 chunk 228 optimal weight: 10.0000 chunk 101 optimal weight: 0.9980 chunk 235 optimal weight: 10.0000 chunk 217 optimal weight: 0.5980 chunk 242 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 7 optimal weight: 0.5980 chunk 121 optimal weight: 0.0770 chunk 67 optimal weight: 8.9990 chunk 71 optimal weight: 0.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 247 ASN F 102 GLN ** J 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.135868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.105124 restraints weight = 35084.452| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.68 r_work: 0.2892 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.419 30965 Z= 0.141 Angle : 0.684 8.866 43945 Z= 0.285 Chirality : 0.049 0.360 3718 Planarity : 0.005 0.043 5852 Dihedral : 17.013 82.000 5201 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 1.04 % Allowed : 17.00 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.16), residues: 2629 helix: 1.04 (0.14), residues: 1430 sheet: None (None), residues: 0 loop : -2.81 (0.16), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 89 TYR 0.011 0.001 TYR E 112 PHE 0.013 0.001 PHE A 230 TRP 0.009 0.001 TRP H 100 HIS 0.002 0.001 HIS E 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 (30921) covalent geometry : angle 0.68365 / 0.29 (43945) hydrogen bonds : bond 0.04159 / 2.79 ( 946) hydrogen bonds : angle 3.54893 / 2.50 ( 2805) Misc. bond : bond 0.20835 / 13.09 ( 44) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 399 time to evaluate : 0.892 Fit side-chains REVERT: A 106 ASP cc_start: 0.7598 (m-30) cc_final: 0.7293 (t0) REVERT: A 132 MET cc_start: 0.8680 (mtm) cc_final: 0.8417 (mtp) REVERT: B 115 SER cc_start: 0.8723 (t) cc_final: 0.8464 (m) REVERT: C 200 ASP cc_start: 0.8245 (OUTLIER) cc_final: 0.7906 (t0) REVERT: C 213 ASP cc_start: 0.9032 (p0) cc_final: 0.8768 (p0) REVERT: C 228 LEU cc_start: 0.8417 (pt) cc_final: 0.8034 (mt) REVERT: C 290 LYS cc_start: 0.7324 (mtpp) cc_final: 0.7064 (ttpt) REVERT: D 180 LYS cc_start: 0.8707 (tptt) cc_final: 0.8388 (tptm) REVERT: D 213 ASP cc_start: 0.8959 (p0) cc_final: 0.8704 (p0) REVERT: E 200 ASP cc_start: 0.8245 (OUTLIER) cc_final: 0.7969 (t0) REVERT: E 290 LYS cc_start: 0.7530 (mtpp) cc_final: 0.7217 (ttmt) REVERT: F 106 ASP cc_start: 0.7745 (m-30) cc_final: 0.7528 (t0) REVERT: F 115 SER cc_start: 0.8974 (t) cc_final: 0.8706 (m) REVERT: F 180 LYS cc_start: 0.8677 (tptm) cc_final: 0.8413 (tptt) REVERT: G 56 GLU cc_start: 0.7421 (mt-10) cc_final: 0.7024 (mt-10) REVERT: G 180 LYS cc_start: 0.8590 (tptt) cc_final: 0.8130 (tptm) REVERT: G 245 ILE cc_start: 0.8235 (mm) cc_final: 0.8018 (mt) REVERT: H 180 LYS cc_start: 0.8718 (tptt) cc_final: 0.8333 (tptm) REVERT: H 206 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8151 (mt-10) REVERT: H 250 ASP cc_start: 0.7749 (m-30) cc_final: 0.7297 (t0) REVERT: I 56 GLU cc_start: 0.7073 (mt-10) cc_final: 0.6712 (mt-10) REVERT: I 106 ASP cc_start: 0.7836 (m-30) cc_final: 0.7515 (t0) REVERT: I 115 SER cc_start: 0.8796 (t) cc_final: 0.8590 (m) REVERT: I 180 LYS cc_start: 0.8607 (tptt) cc_final: 0.8099 (tptm) REVERT: I 184 ASN cc_start: 0.8134 (m-40) cc_final: 0.7927 (m110) REVERT: I 190 GLU cc_start: 0.8310 (tt0) cc_final: 0.7955 (tt0) REVERT: I 200 ASP cc_start: 0.8678 (OUTLIER) cc_final: 0.8272 (t0) REVERT: I 213 ASP cc_start: 0.8982 (p0) cc_final: 0.8570 (p0) REVERT: I 250 ASP cc_start: 0.7832 (m-30) cc_final: 0.7459 (m-30) REVERT: J 183 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7984 (tp30) outliers start: 22 outliers final: 11 residues processed: 413 average time/residue: 0.1927 time to fit residues: 126.1636 Evaluate side-chains 389 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 375 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain E residue 200 ASP Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain I residue 200 ASP Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain K residue 210 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 218 optimal weight: 0.0170 chunk 182 optimal weight: 9.9990 chunk 54 optimal weight: 0.8980 chunk 94 optimal weight: 9.9990 chunk 148 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 115 optimal weight: 8.9990 chunk 167 optimal weight: 0.2980 chunk 23 optimal weight: 0.8980 chunk 191 optimal weight: 8.9990 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 247 ASN F 102 GLN J 184 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.137847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.107062 restraints weight = 35261.819| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.69 r_work: 0.2839 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.391 30965 Z= 0.133 Angle : 0.646 9.425 43945 Z= 0.269 Chirality : 0.046 0.316 3718 Planarity : 0.005 0.048 5852 Dihedral : 16.278 62.813 5198 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 1.37 % Allowed : 16.25 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.17), residues: 2629 helix: 1.54 (0.14), residues: 1419 sheet: None (None), residues: 0 loop : -2.69 (0.16), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 89 TYR 0.009 0.001 TYR E 112 PHE 0.015 0.001 PHE A 230 TRP 0.012 0.001 TRP K 149 HIS 0.002 0.001 HIS J 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (30921) covalent geometry : angle 0.64554 / 0.27 (43945) hydrogen bonds : bond 0.03786 / 2.56 ( 946) hydrogen bonds : angle 3.31905 / 2.34 ( 2805) Misc. bond : bond 0.19282 / 12.09 ( 44) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 407 time to evaluate : 0.899 Fit side-chains REVERT: A 56 GLU cc_start: 0.7364 (mt-10) cc_final: 0.7135 (pt0) REVERT: A 106 ASP cc_start: 0.7650 (m-30) cc_final: 0.7333 (t0) REVERT: A 132 MET cc_start: 0.8645 (mtm) cc_final: 0.8315 (mtp) REVERT: A 228 LEU cc_start: 0.8480 (pt) cc_final: 0.8238 (mt) REVERT: A 290 LYS cc_start: 0.7701 (mtpp) cc_final: 0.7486 (ttpt) REVERT: B 115 SER cc_start: 0.8731 (t) cc_final: 0.8459 (m) REVERT: B 228 LEU cc_start: 0.8593 (pt) cc_final: 0.8127 (mt) REVERT: B 290 LYS cc_start: 0.7460 (mtpp) cc_final: 0.7027 (ttmt) REVERT: C 200 ASP cc_start: 0.8046 (OUTLIER) cc_final: 0.7727 (t0) REVERT: C 213 ASP cc_start: 0.9018 (p0) cc_final: 0.8691 (p0) REVERT: C 228 LEU cc_start: 0.8596 (pt) cc_final: 0.8289 (mt) REVERT: C 290 LYS cc_start: 0.7360 (mtpp) cc_final: 0.6986 (ttpt) REVERT: D 180 LYS cc_start: 0.8735 (tptt) cc_final: 0.8380 (tptm) REVERT: E 180 LYS cc_start: 0.8505 (tptt) cc_final: 0.8203 (tptm) REVERT: E 200 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7925 (t0) REVERT: E 228 LEU cc_start: 0.8685 (pt) cc_final: 0.8194 (mt) REVERT: F 106 ASP cc_start: 0.7829 (m-30) cc_final: 0.7536 (t0) REVERT: F 115 SER cc_start: 0.8956 (t) cc_final: 0.8680 (m) REVERT: F 180 LYS cc_start: 0.8651 (tptm) cc_final: 0.8380 (tptm) REVERT: F 228 LEU cc_start: 0.8476 (pt) cc_final: 0.8173 (mt) REVERT: G 56 GLU cc_start: 0.7261 (mt-10) cc_final: 0.6917 (mt-10) REVERT: G 180 LYS cc_start: 0.8567 (tptt) cc_final: 0.8159 (tptm) REVERT: G 228 LEU cc_start: 0.8612 (pt) cc_final: 0.8249 (mt) REVERT: G 250 ASP cc_start: 0.7622 (m-30) cc_final: 0.7357 (m-30) REVERT: H 132 MET cc_start: 0.9026 (mtm) cc_final: 0.8715 (mtp) REVERT: H 180 LYS cc_start: 0.8706 (tptt) cc_final: 0.8246 (tptm) REVERT: I 56 GLU cc_start: 0.7091 (mt-10) cc_final: 0.6666 (mt-10) REVERT: I 106 ASP cc_start: 0.7936 (m-30) cc_final: 0.7533 (t0) REVERT: I 180 LYS cc_start: 0.8579 (tptt) cc_final: 0.8097 (tptm) REVERT: I 190 GLU cc_start: 0.8356 (tt0) cc_final: 0.7949 (tt0) REVERT: I 200 ASP cc_start: 0.8535 (OUTLIER) cc_final: 0.8097 (t0) REVERT: I 213 ASP cc_start: 0.8979 (p0) cc_final: 0.8769 (p0) REVERT: I 228 LEU cc_start: 0.8455 (pt) cc_final: 0.8184 (mt) REVERT: I 250 ASP cc_start: 0.7832 (m-30) cc_final: 0.7464 (m-30) REVERT: I 290 LYS cc_start: 0.7529 (mtpp) cc_final: 0.7254 (ttpt) REVERT: J 228 LEU cc_start: 0.8757 (pt) cc_final: 0.8348 (mt) outliers start: 29 outliers final: 10 residues processed: 431 average time/residue: 0.1812 time to fit residues: 126.7107 Evaluate side-chains 404 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 391 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain E residue 200 ASP Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain I residue 200 ASP Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain K residue 210 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 77 optimal weight: 10.0000 chunk 118 optimal weight: 6.9990 chunk 153 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 238 optimal weight: 8.9990 chunk 225 optimal weight: 0.0020 chunk 251 optimal weight: 6.9990 chunk 167 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 chunk 199 optimal weight: 0.1980 overall best weight: 3.0394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 184 ASN F 102 GLN F 184 ASN G 184 ASN I 247 ASN ** J 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.129973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.098803 restraints weight = 35206.163| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 1.69 r_work: 0.2776 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.493 30965 Z= 0.222 Angle : 0.805 12.176 43945 Z= 0.332 Chirality : 0.056 0.363 3718 Planarity : 0.006 0.055 5852 Dihedral : 16.848 72.303 5198 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 2.07 % Allowed : 17.00 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.17), residues: 2629 helix: 1.28 (0.14), residues: 1441 sheet: None (None), residues: 0 loop : -2.72 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 221 TYR 0.012 0.002 TYR E 112 PHE 0.021 0.002 PHE B 230 TRP 0.007 0.001 TRP H 149 HIS 0.004 0.001 HIS I 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.20 (30921) covalent geometry : angle 0.80489 / 0.33 (43945) hydrogen bonds : bond 0.05120 / 3.46 ( 946) hydrogen bonds : angle 3.53846 / 2.49 ( 2805) Misc. bond : bond 0.23971 / 15.11 ( 44) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 407 time to evaluate : 0.861 Fit side-chains REVERT: A 56 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7163 (pt0) REVERT: A 106 ASP cc_start: 0.7632 (m-30) cc_final: 0.7330 (t0) REVERT: A 132 MET cc_start: 0.8701 (mtm) cc_final: 0.8209 (mtp) REVERT: A 213 ASP cc_start: 0.9061 (p0) cc_final: 0.8774 (p0) REVERT: B 115 SER cc_start: 0.8944 (t) cc_final: 0.8661 (m) REVERT: B 290 LYS cc_start: 0.7590 (mtpp) cc_final: 0.7128 (ttmt) REVERT: C 200 ASP cc_start: 0.8344 (OUTLIER) cc_final: 0.7961 (t0) REVERT: C 213 ASP cc_start: 0.9098 (p0) cc_final: 0.8755 (p0) REVERT: C 290 LYS cc_start: 0.7553 (mtpp) cc_final: 0.7260 (ttpt) REVERT: D 180 LYS cc_start: 0.8785 (tptt) cc_final: 0.8429 (tptm) REVERT: D 254 SER cc_start: 0.8344 (p) cc_final: 0.8105 (p) REVERT: E 180 LYS cc_start: 0.8615 (tptt) cc_final: 0.8082 (tptm) REVERT: F 106 ASP cc_start: 0.7877 (m-30) cc_final: 0.7563 (t0) REVERT: F 115 SER cc_start: 0.9152 (t) cc_final: 0.8898 (m) REVERT: F 180 LYS cc_start: 0.8656 (tptm) cc_final: 0.8447 (tptm) REVERT: G 56 GLU cc_start: 0.7421 (mt-10) cc_final: 0.7034 (mt-10) REVERT: G 180 LYS cc_start: 0.8592 (tptt) cc_final: 0.8111 (tptm) REVERT: H 132 MET cc_start: 0.8976 (mtm) cc_final: 0.8684 (mtp) REVERT: H 180 LYS cc_start: 0.8716 (tptt) cc_final: 0.8296 (tptm) REVERT: I 56 GLU cc_start: 0.7305 (mt-10) cc_final: 0.6936 (mt-10) REVERT: I 106 ASP cc_start: 0.7833 (m-30) cc_final: 0.7530 (t0) REVERT: I 180 LYS cc_start: 0.8489 (tptt) cc_final: 0.8079 (tptm) REVERT: I 190 GLU cc_start: 0.8404 (tt0) cc_final: 0.8028 (tt0) REVERT: I 200 ASP cc_start: 0.8693 (OUTLIER) cc_final: 0.8320 (t0) REVERT: I 213 ASP cc_start: 0.9021 (p0) cc_final: 0.8610 (p0) REVERT: I 250 ASP cc_start: 0.7871 (m-30) cc_final: 0.7503 (m-30) REVERT: I 290 LYS cc_start: 0.7603 (mtpp) cc_final: 0.7348 (ttpt) REVERT: J 254 SER cc_start: 0.8503 (p) cc_final: 0.8233 (p) outliers start: 44 outliers final: 26 residues processed: 433 average time/residue: 0.1810 time to fit residues: 126.3969 Evaluate side-chains 434 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 406 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 281 MET Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain I residue 200 ASP Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 187 GLU Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain K residue 206 GLU Chi-restraints excluded: chain K residue 210 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 245 optimal weight: 0.9990 chunk 214 optimal weight: 6.9990 chunk 260 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 247 optimal weight: 0.2980 chunk 136 optimal weight: 7.9990 chunk 192 optimal weight: 10.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 102 GLN J 184 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.135480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.104481 restraints weight = 35094.620| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.69 r_work: 0.2881 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.418 30965 Z= 0.143 Angle : 0.688 10.481 43945 Z= 0.290 Chirality : 0.048 0.328 3718 Planarity : 0.005 0.069 5852 Dihedral : 16.296 67.263 5196 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 1.41 % Allowed : 18.18 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.17), residues: 2629 helix: 1.61 (0.14), residues: 1441 sheet: None (None), residues: 0 loop : -2.64 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 89 TYR 0.011 0.001 TYR E 112 PHE 0.016 0.001 PHE F 174 TRP 0.009 0.001 TRP K 149 HIS 0.002 0.001 HIS J 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (30921) covalent geometry : angle 0.68751 / 0.29 (43945) hydrogen bonds : bond 0.04342 / 2.85 ( 946) hydrogen bonds : angle 3.40655 / 2.39 ( 2805) Misc. bond : bond 0.20692 / 12.98 ( 44) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 380 time to evaluate : 0.869 Fit side-chains REVERT: A 56 GLU cc_start: 0.7446 (mt-10) cc_final: 0.7189 (pt0) REVERT: A 106 ASP cc_start: 0.7582 (m-30) cc_final: 0.7334 (t0) REVERT: A 132 MET cc_start: 0.8652 (mtp) cc_final: 0.8306 (mtp) REVERT: B 115 SER cc_start: 0.8799 (t) cc_final: 0.8549 (m) REVERT: B 290 LYS cc_start: 0.7534 (mtpp) cc_final: 0.7163 (ttmt) REVERT: C 200 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7891 (t0) REVERT: C 213 ASP cc_start: 0.9078 (p0) cc_final: 0.8730 (p0) REVERT: C 290 LYS cc_start: 0.7465 (mtpp) cc_final: 0.7190 (ttpt) REVERT: D 180 LYS cc_start: 0.8759 (tptt) cc_final: 0.8416 (tptm) REVERT: D 254 SER cc_start: 0.8411 (p) cc_final: 0.8205 (p) REVERT: E 180 LYS cc_start: 0.8607 (tptt) cc_final: 0.8127 (tptm) REVERT: F 115 SER cc_start: 0.9063 (t) cc_final: 0.8818 (m) REVERT: G 56 GLU cc_start: 0.7315 (mt-10) cc_final: 0.7004 (mt-10) REVERT: G 180 LYS cc_start: 0.8595 (tptt) cc_final: 0.8264 (tptp) REVERT: G 183 GLU cc_start: 0.8432 (tp30) cc_final: 0.8188 (tp30) REVERT: G 228 LEU cc_start: 0.8687 (pt) cc_final: 0.8250 (mt) REVERT: H 132 MET cc_start: 0.8960 (mtm) cc_final: 0.8652 (mtp) REVERT: H 180 LYS cc_start: 0.8704 (tptt) cc_final: 0.8277 (tptm) REVERT: I 56 GLU cc_start: 0.7118 (mt-10) cc_final: 0.6797 (mt-10) REVERT: I 106 ASP cc_start: 0.7821 (m-30) cc_final: 0.7579 (t0) REVERT: I 190 GLU cc_start: 0.8345 (tt0) cc_final: 0.7970 (tt0) REVERT: I 200 ASP cc_start: 0.8619 (OUTLIER) cc_final: 0.8251 (t0) REVERT: I 213 ASP cc_start: 0.8999 (p0) cc_final: 0.8553 (p0) REVERT: I 288 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.8439 (tmm160) REVERT: J 228 LEU cc_start: 0.8810 (pt) cc_final: 0.8459 (mt) REVERT: J 254 SER cc_start: 0.8467 (p) cc_final: 0.8215 (p) REVERT: K 142 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7768 (tt0) outliers start: 30 outliers final: 19 residues processed: 403 average time/residue: 0.1809 time to fit residues: 116.9425 Evaluate side-chains 397 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 375 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 281 MET Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 265 ASP Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain I residue 200 ASP Chi-restraints excluded: chain I residue 288 ARG Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain K residue 210 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 247 optimal weight: 4.9990 chunk 234 optimal weight: 0.5980 chunk 10 optimal weight: 6.9990 chunk 86 optimal weight: 9.9990 chunk 232 optimal weight: 8.9990 chunk 3 optimal weight: 0.0060 chunk 224 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 17 optimal weight: 0.0970 chunk 36 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 overall best weight: 1.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 184 ASN F 102 GLN G 184 ASN I 247 ASN ** J 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.133076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.101885 restraints weight = 35349.505| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.69 r_work: 0.2843 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.444 30965 Z= 0.175 Angle : 0.741 11.984 43945 Z= 0.311 Chirality : 0.051 0.338 3718 Planarity : 0.006 0.106 5852 Dihedral : 16.370 69.728 5196 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 1.74 % Allowed : 17.95 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.17), residues: 2629 helix: 1.62 (0.14), residues: 1441 sheet: None (None), residues: 0 loop : -2.59 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 221 TYR 0.010 0.001 TYR E 112 PHE 0.016 0.001 PHE K 174 TRP 0.009 0.001 TRP K 149 HIS 0.003 0.001 HIS I 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (30921) covalent geometry : angle 0.74086 / 0.31 (43945) hydrogen bonds : bond 0.04679 / 3.11 ( 946) hydrogen bonds : angle 3.42540 / 2.41 ( 2805) Misc. bond : bond 0.21754 / 13.67 ( 44) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 384 time to evaluate : 0.870 Fit side-chains REVERT: A 56 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7225 (pt0) REVERT: A 106 ASP cc_start: 0.7588 (m-30) cc_final: 0.7332 (t0) REVERT: A 132 MET cc_start: 0.8645 (mtp) cc_final: 0.8218 (mtp) REVERT: A 242 LYS cc_start: 0.8472 (mttm) cc_final: 0.7793 (mtmt) REVERT: B 115 SER cc_start: 0.8897 (t) cc_final: 0.8643 (m) REVERT: B 290 LYS cc_start: 0.7558 (mtpp) cc_final: 0.7199 (ttmt) REVERT: C 200 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.7919 (t0) REVERT: C 213 ASP cc_start: 0.9088 (p0) cc_final: 0.8727 (p0) REVERT: C 290 LYS cc_start: 0.7513 (mtpp) cc_final: 0.7278 (ttpt) REVERT: D 180 LYS cc_start: 0.8793 (tptt) cc_final: 0.8473 (tptm) REVERT: D 254 SER cc_start: 0.8419 (p) cc_final: 0.8191 (p) REVERT: E 172 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8064 (mt) REVERT: E 180 LYS cc_start: 0.8608 (tptt) cc_final: 0.8109 (tptm) REVERT: E 206 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8026 (mm-30) REVERT: F 115 SER cc_start: 0.9135 (t) cc_final: 0.8895 (m) REVERT: G 56 GLU cc_start: 0.7394 (mt-10) cc_final: 0.7029 (mt-10) REVERT: G 180 LYS cc_start: 0.8634 (tptt) cc_final: 0.8175 (tptm) REVERT: G 183 GLU cc_start: 0.8442 (tp30) cc_final: 0.8172 (tp30) REVERT: G 228 LEU cc_start: 0.8806 (pt) cc_final: 0.8363 (mt) REVERT: H 132 MET cc_start: 0.8958 (mtm) cc_final: 0.8652 (mtp) REVERT: H 180 LYS cc_start: 0.8724 (tptt) cc_final: 0.8285 (tptm) REVERT: I 56 GLU cc_start: 0.7259 (mt-10) cc_final: 0.6957 (mt-10) REVERT: I 106 ASP cc_start: 0.7838 (m-30) cc_final: 0.7575 (t0) REVERT: I 180 LYS cc_start: 0.8557 (tptt) cc_final: 0.8316 (tptm) REVERT: I 190 GLU cc_start: 0.8408 (tt0) cc_final: 0.8033 (tt0) REVERT: I 200 ASP cc_start: 0.8655 (OUTLIER) cc_final: 0.8271 (t0) REVERT: I 213 ASP cc_start: 0.9007 (p0) cc_final: 0.8585 (p0) REVERT: J 180 LYS cc_start: 0.8654 (tptt) cc_final: 0.8304 (tptp) REVERT: J 228 LEU cc_start: 0.8795 (pt) cc_final: 0.8400 (mt) REVERT: J 254 SER cc_start: 0.8498 (p) cc_final: 0.8234 (p) REVERT: K 142 GLU cc_start: 0.8052 (tm-30) cc_final: 0.7744 (tt0) REVERT: K 172 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8147 (mt) outliers start: 37 outliers final: 25 residues processed: 412 average time/residue: 0.1866 time to fit residues: 122.9371 Evaluate side-chains 405 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 376 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 281 MET Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 265 ASP Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain I residue 200 ASP Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain K residue 172 LEU Chi-restraints excluded: chain K residue 210 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 61 optimal weight: 7.9990 chunk 127 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 164 optimal weight: 5.9990 chunk 214 optimal weight: 8.9990 chunk 115 optimal weight: 5.9990 chunk 142 optimal weight: 8.9990 chunk 241 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 184 ASN C 184 ASN F 102 GLN F 184 ASN ** J 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.126358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.094717 restraints weight = 35605.820| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.71 r_work: 0.2750 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.498 30965 Z= 0.269 Angle : 0.903 14.308 43945 Z= 0.375 Chirality : 0.061 0.394 3718 Planarity : 0.007 0.088 5852 Dihedral : 17.121 79.866 5196 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.27 % Favored : 89.73 % Rotamer: Outliers : 1.65 % Allowed : 18.23 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.17), residues: 2629 helix: 1.27 (0.14), residues: 1441 sheet: None (None), residues: 0 loop : -2.75 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 288 TYR 0.014 0.002 TYR F 68 PHE 0.025 0.002 PHE B 230 TRP 0.010 0.002 TRP K 149 HIS 0.005 0.001 HIS I 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.25 (30921) covalent geometry : angle 0.90349 / 0.38 (43945) hydrogen bonds : bond 0.05806 / 3.89 ( 946) hydrogen bonds : angle 3.65773 / 2.58 ( 2805) Misc. bond : bond 0.24185 / 15.26 ( 44) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 384 time to evaluate : 0.998 Fit side-chains REVERT: A 106 ASP cc_start: 0.7605 (m-30) cc_final: 0.7313 (t0) REVERT: A 246 GLU cc_start: 0.7063 (mp0) cc_final: 0.6809 (mp0) REVERT: B 115 SER cc_start: 0.8971 (t) cc_final: 0.8674 (m) REVERT: B 190 GLU cc_start: 0.8453 (tt0) cc_final: 0.8234 (tt0) REVERT: B 290 LYS cc_start: 0.7740 (mtpp) cc_final: 0.7375 (ttmt) REVERT: C 200 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.7933 (t0) REVERT: C 213 ASP cc_start: 0.9204 (p0) cc_final: 0.8830 (p0) REVERT: D 254 SER cc_start: 0.8325 (p) cc_final: 0.8079 (p) REVERT: E 172 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8099 (mt) REVERT: E 180 LYS cc_start: 0.8588 (tptt) cc_final: 0.7992 (tptm) REVERT: F 115 SER cc_start: 0.9218 (t) cc_final: 0.8955 (m) REVERT: F 180 LYS cc_start: 0.8580 (tptm) cc_final: 0.8332 (tptt) REVERT: G 180 LYS cc_start: 0.8638 (tptt) cc_final: 0.8336 (tptp) REVERT: G 183 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8091 (tp30) REVERT: H 132 MET cc_start: 0.8947 (mtm) cc_final: 0.8722 (mtp) REVERT: H 180 LYS cc_start: 0.8763 (tptt) cc_final: 0.8336 (tptm) REVERT: I 56 GLU cc_start: 0.7442 (mt-10) cc_final: 0.7087 (mt-10) REVERT: I 106 ASP cc_start: 0.7811 (m-30) cc_final: 0.7529 (t0) REVERT: I 213 ASP cc_start: 0.9085 (p0) cc_final: 0.8758 (p0) REVERT: J 254 SER cc_start: 0.8485 (p) cc_final: 0.8176 (p) REVERT: K 172 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8108 (mt) outliers start: 35 outliers final: 25 residues processed: 407 average time/residue: 0.1815 time to fit residues: 118.7389 Evaluate side-chains 406 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 377 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 281 MET Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 265 ASP Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 187 GLU Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain K residue 172 LEU Chi-restraints excluded: chain K residue 206 GLU Chi-restraints excluded: chain K residue 210 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 60 optimal weight: 4.9990 chunk 263 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 151 optimal weight: 0.5980 chunk 123 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 233 optimal weight: 0.6980 chunk 239 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 126 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 184 ASN F 102 GLN G 184 ASN ** J 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.132241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.100596 restraints weight = 35123.687| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 1.72 r_work: 0.2824 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.428 30965 Z= 0.155 Angle : 0.743 15.477 43945 Z= 0.317 Chirality : 0.050 0.348 3718 Planarity : 0.006 0.125 5852 Dihedral : 16.429 74.243 5194 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 1.27 % Allowed : 18.61 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.17), residues: 2629 helix: 1.65 (0.14), residues: 1441 sheet: None (None), residues: 0 loop : -2.70 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 288 TYR 0.011 0.001 TYR E 112 PHE 0.016 0.001 PHE C 174 TRP 0.012 0.001 TRP K 149 HIS 0.002 0.001 HIS C 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (30921) covalent geometry : angle 0.74326 / 0.32 (43945) hydrogen bonds : bond 0.04690 / 3.09 ( 946) hydrogen bonds : angle 3.46933 / 2.44 ( 2805) Misc. bond : bond 0.21148 / 13.28 ( 44) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 380 time to evaluate : 1.020 Fit side-chains revert: symmetry clash REVERT: A 106 ASP cc_start: 0.7648 (m-30) cc_final: 0.7335 (t0) REVERT: B 115 SER cc_start: 0.8783 (t) cc_final: 0.8542 (m) REVERT: B 290 LYS cc_start: 0.7689 (mtpp) cc_final: 0.7361 (ttmt) REVERT: C 200 ASP cc_start: 0.8344 (OUTLIER) cc_final: 0.7858 (t0) REVERT: C 213 ASP cc_start: 0.9130 (p0) cc_final: 0.8781 (p0) REVERT: D 180 LYS cc_start: 0.8775 (tptt) cc_final: 0.8497 (tptm) REVERT: D 254 SER cc_start: 0.8404 (p) cc_final: 0.8187 (p) REVERT: E 172 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7998 (mt) REVERT: E 180 LYS cc_start: 0.8517 (tptt) cc_final: 0.8073 (tptm) REVERT: E 206 GLU cc_start: 0.8385 (mt-10) cc_final: 0.7953 (mm-30) REVERT: F 115 SER cc_start: 0.9081 (t) cc_final: 0.8841 (m) REVERT: F 180 LYS cc_start: 0.8555 (tptm) cc_final: 0.8298 (tptt) REVERT: F 228 LEU cc_start: 0.8717 (pt) cc_final: 0.8336 (mt) REVERT: G 56 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7188 (mt-10) REVERT: G 228 LEU cc_start: 0.8718 (pt) cc_final: 0.8332 (mt) REVERT: H 132 MET cc_start: 0.8932 (mtm) cc_final: 0.8679 (mtp) REVERT: I 106 ASP cc_start: 0.7864 (m-30) cc_final: 0.7560 (t0) REVERT: I 190 GLU cc_start: 0.8409 (tt0) cc_final: 0.8044 (tt0) REVERT: I 213 ASP cc_start: 0.9047 (p0) cc_final: 0.8561 (p0) REVERT: J 180 LYS cc_start: 0.8453 (tptt) cc_final: 0.8123 (tptp) REVERT: J 228 LEU cc_start: 0.8836 (pt) cc_final: 0.8512 (mt) REVERT: J 254 SER cc_start: 0.8477 (p) cc_final: 0.8215 (p) REVERT: K 142 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7839 (tt0) REVERT: K 172 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8062 (mt) REVERT: K 228 LEU cc_start: 0.8629 (pt) cc_final: 0.8364 (mt) outliers start: 27 outliers final: 22 residues processed: 399 average time/residue: 0.1898 time to fit residues: 121.9230 Evaluate side-chains 393 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 368 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 281 MET Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 290 LYS Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 265 ASP Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain K residue 172 LEU Chi-restraints excluded: chain K residue 210 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 160 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 206 optimal weight: 0.9990 chunk 120 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 118 optimal weight: 7.9990 chunk 189 optimal weight: 4.9990 chunk 88 optimal weight: 9.9990 chunk 216 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 29 optimal weight: 0.5980 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 102 GLN F 184 ASN ** J 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.127634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.095839 restraints weight = 35666.265| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 1.72 r_work: 0.2731 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2588 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.478 30965 Z= 0.229 Angle : 0.852 13.776 43945 Z= 0.358 Chirality : 0.057 0.379 3718 Planarity : 0.007 0.119 5852 Dihedral : 16.830 78.906 5194 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.12 % Favored : 89.88 % Rotamer: Outliers : 1.55 % Allowed : 18.51 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.17), residues: 2629 helix: 1.46 (0.14), residues: 1441 sheet: None (None), residues: 0 loop : -2.72 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 288 TYR 0.012 0.002 TYR F 68 PHE 0.021 0.002 PHE B 230 TRP 0.018 0.002 TRP K 149 HIS 0.004 0.001 HIS I 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.21 (30921) covalent geometry : angle 0.85217 / 0.36 (43945) hydrogen bonds : bond 0.05431 / 3.64 ( 946) hydrogen bonds : angle 3.55435 / 2.51 ( 2805) Misc. bond : bond 0.23440 / 14.78 ( 44) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7104.22 seconds wall clock time: 122 minutes 8.90 seconds (7328.90 seconds total)